Guild Wars 2

Take a look at how EQ2 did it.

Skills were balanced seperately around what they were hitting.

Hitting an NPC? Stun for 3 seconds, do 1000 damage.
Hit a player? Stun for 1.5 Seconds, do 500 damage.

Just do this and suddenly you can keep both sides of the game happy.

The argument “it would be confusing for new players” is null and void, they’ll never learn these things if they’re continually treated like babies with no braincells.

Your example is exacly how GW1 handled balance between PvP/E.

Some skills were split between PvP and PvE before last patch and I think some still are.
Split wasn’t problem, but the fact that skills with +/-% damage multipers in PvP/PvE wasn’t written in skill description.